Formatting

[jalview.git] / src / jalview / schemes / Consensus.java

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 27c5906..8aa59e3 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,77 +1,79 @@
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.schemes;\r
 \r
 ////////////////////////////////////////////\r
 // This does nothing at all at the moment!!!!!!!!!!\r
 // AW 15th Dec 2004\r
 /////////////////////////////////////////\r
-public class Consensus {\r
-\r
+public class Consensus\r
+{\r
   int[] mask;\r
   double threshold;\r
-   String maskstr;\r
+  String maskstr;\r
 \r
-  public Consensus(String mask, double threshold) {\r
+  public Consensus(String mask, double threshold)\r
+  {\r
     // this.id = id;\r
     //    this.mask = mask;\r
-        this.maskstr = mask;\r
+    this.maskstr = mask;\r
     setMask(mask);\r
     this.threshold = threshold;\r
   }\r
 \r
-  public void setMask(String s) {\r
+  public void setMask(String s)\r
+  {\r
     this.mask = setNums(s);\r
+\r
     //   for (int i=0; i < mask.length; i++) {\r
     //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
     // }\r
   }\r
 \r
-  public boolean isConserved(int[][] cons2,int col ,int size) {\r
+  public boolean isConserved(int[][] cons2, int col, int size)\r
+  {\r
     int tot = 0;\r
+\r
     for (int i = 0; i < mask.length; i++)\r
+    {\r
       tot += cons2[col][mask[i]];\r
+    }\r
 \r
-    if ( (double) tot > threshold * size / 100)\r
+    if ( (double) tot > ( (threshold * size) / 100))\r
+    {\r
       return true;\r
+    }\r
 \r
     return false;\r
   }\r
 \r
   int[] setNums(String s)\r
   {\r
-    int [] out = new int[s.length()];\r
+    int[] out = new int[s.length()];\r
     int i = 0;\r
+\r
     while (i < s.length())\r
     {\r
-      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
+      out[i] = ResidueProperties.aaIndex[s.charAt(i)];\r
       i++;\r
-\r
     }\r
 \r
     return out;\r
   }\r
-\r
-\r
 }\r
-\r
-\r
-\r
-\r